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- PDB-4qnc: Crystal structure of a SemiSWEET in an occluded state -

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Basic information

Entry
Database: PDB / ID: 4qnc
TitleCrystal structure of a SemiSWEET in an occluded state
Componentschemical transport protein
KeywordsMEMBRANE PROTEIN / transporter
Function / homology
Function and homology information


D-glucose transmembrane transporter activity / D-glucose transmembrane transport / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Monooxygenase - #290 / : / PQ-loop repeat / PQ loop repeat / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PENTADECANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sugar transporter SemiSWEET
Similarity search - Component
Biological speciesLeptospira biflexa serovar Patoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.388 Å
AuthorsYan, X. / Yuyong, T. / Liang, F. / Perry, K.
CitationJournal: Nature / Year: 2014
Title: Structures of bacterial homologues of SWEET transporters in two distinct conformations.
Authors: Xu, Y. / Tao, Y. / Cheung, L.S. / Fan, C. / Chen, L.Q. / Xu, S. / Perry, K. / Frommer, W.B. / Feng, L.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chemical transport protein
B: chemical transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,72510
Polymers21,4502
Non-polymers2,2768
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-32 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.907, 51.833, 46.963
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein chemical transport protein


Mass: 10724.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira biflexa serovar Patoc (bacteria)
Strain: Patoc 1 / ATCC 23582 / Paris / Gene: LEPBI_I1613 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0SR19
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H32
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 11

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 100mM HEPES pH7.5, 150mM (NH4)2SO4, 10% PEG400, lipid cubic phase, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.9794
SYNCHROTRONAPS 23-ID-B20.9794
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDAug 16, 2013
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal cryo-cooled Si(111)SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.388→50 Å / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.203 / Rsym value: 0.203 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Rsym value: 0.556 / % possible all: 79.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.388→36.774 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 32.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2758 310 4.64 %
Rwork0.2662 --
obs0.2666 6684 93.84 %
all-6683 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.388→36.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 146 14 1492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051500
X-RAY DIFFRACTIONf_angle_d0.9751992
X-RAY DIFFRACTIONf_dihedral_angle_d22.176608
X-RAY DIFFRACTIONf_chiral_restr0.046231
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.388-3.00840.33351580.29243034X-RAY DIFFRACTION91
3.0084-36.77820.25271520.25773340X-RAY DIFFRACTION97

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